Starting phenix.real_space_refine on Sun Feb 18 11:42:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/02_2024/8glj_40195_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/02_2024/8glj_40195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/02_2024/8glj_40195.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/02_2024/8glj_40195.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/02_2024/8glj_40195_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8glj_40195/02_2024/8glj_40195_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 13843 2.51 5 N 3662 2.21 5 O 4340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21891 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2191, 17380 Classifications: {'peptide': 2191} Link IDs: {'PCIS': 3, 'PTRANS': 99, 'TRANS': 2088} Chain breaks: 3 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2861 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "D" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 591 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.22, per 1000 atoms: 0.51 Number of scatterers: 21891 At special positions: 0 Unit cell: (119.19, 128.232, 135.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 4340 8.00 N 3662 7.00 C 13843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.76 Conformation dependent library (CDL) restraints added in 4.0 seconds 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5116 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 30 sheets defined 10.5% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.38 Creating SS restraints... Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 296 through 305 removed outlier: 4.581A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 402 through 405 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 518 through 522 removed outlier: 3.591A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 518 through 522' Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 651 through 654 No H-bonds generated for 'chain 'A' and resid 651 through 654' Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 664 through 667 No H-bonds generated for 'chain 'A' and resid 664 through 667' Processing helix chain 'A' and resid 731 through 736 removed outlier: 3.825A pdb=" N ALA A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER A 736 " --> pdb=" O SER A 732 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 731 through 736' Processing helix chain 'A' and resid 811 through 818 Processing helix chain 'A' and resid 846 through 848 No H-bonds generated for 'chain 'A' and resid 846 through 848' Processing helix chain 'A' and resid 899 through 902 Processing helix chain 'A' and resid 915 through 917 No H-bonds generated for 'chain 'A' and resid 915 through 917' Processing helix chain 'A' and resid 940 through 943 No H-bonds generated for 'chain 'A' and resid 940 through 943' Processing helix chain 'A' and resid 983 through 985 No H-bonds generated for 'chain 'A' and resid 983 through 985' Processing helix chain 'A' and resid 999 through 1002 No H-bonds generated for 'chain 'A' and resid 999 through 1002' Processing helix chain 'A' and resid 1049 through 1051 No H-bonds generated for 'chain 'A' and resid 1049 through 1051' Processing helix chain 'A' and resid 1082 through 1088 Processing helix chain 'A' and resid 1100 through 1103 No H-bonds generated for 'chain 'A' and resid 1100 through 1103' Processing helix chain 'A' and resid 1105 through 1107 No H-bonds generated for 'chain 'A' and resid 1105 through 1107' Processing helix chain 'A' and resid 1128 through 1131 No H-bonds generated for 'chain 'A' and resid 1128 through 1131' Processing helix chain 'A' and resid 1413 through 1416 No H-bonds generated for 'chain 'A' and resid 1413 through 1416' Processing helix chain 'A' and resid 1427 through 1439 removed outlier: 4.307A pdb=" N SER A1439 " --> pdb=" O ILE A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1455 through 1457 No H-bonds generated for 'chain 'A' and resid 1455 through 1457' Processing helix chain 'A' and resid 1572 through 1575 Processing helix chain 'A' and resid 1578 through 1580 No H-bonds generated for 'chain 'A' and resid 1578 through 1580' Processing helix chain 'A' and resid 1608 through 1613 Processing helix chain 'A' and resid 1618 through 1628 Processing helix chain 'A' and resid 1657 through 1659 No H-bonds generated for 'chain 'A' and resid 1657 through 1659' Processing helix chain 'A' and resid 1857 through 1860 No H-bonds generated for 'chain 'A' and resid 1857 through 1860' Processing helix chain 'A' and resid 1977 through 1981 removed outlier: 3.797A pdb=" N PHE A1981 " --> pdb=" O LEU A1977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1977 through 1981' Processing helix chain 'A' and resid 1988 through 1994 Processing helix chain 'A' and resid 2072 through 2074 No H-bonds generated for 'chain 'A' and resid 2072 through 2074' Processing helix chain 'A' and resid 2085 through 2105 removed outlier: 3.693A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2128 through 2135 removed outlier: 4.362A pdb=" N ALA A2131 " --> pdb=" O PRO A2128 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A2132 " --> pdb=" O ASN A2129 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A2135 " --> pdb=" O VAL A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2159 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2187 through 2191 removed outlier: 4.386A pdb=" N LYS A2191 " --> pdb=" O LEU A2187 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2187 through 2191' Processing helix chain 'B' and resid 28 through 41 Processing helix chain 'B' and resid 127 through 135 Proline residue: B 134 - end of helix Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 39 through 43 Processing helix chain 'F' and resid 62 through 67 removed outlier: 3.928A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 296 Processing helix chain 'F' and resid 300 through 306 removed outlier: 4.023A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.997A pdb=" N LYS F 320 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU F 321 " --> pdb=" O GLU F 317 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 763 through 767 removed outlier: 6.558A pdb=" N PHE A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE A1640 " --> pdb=" O PRO A1585 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N PHE A1662 " --> pdb=" O GLY A1641 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N GLN A1743 " --> pdb=" O ALA A1677 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR A1679 " --> pdb=" O ARG A1741 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG A1741 " --> pdb=" O TYR A1679 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP A1681 " --> pdb=" O SER A1739 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER A1739 " --> pdb=" O ASP A1681 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN A1683 " --> pdb=" O ARG A1737 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG A1737 " --> pdb=" O GLN A1683 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN A1685 " --> pdb=" O ILE A1735 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A1735 " --> pdb=" O ASN A1685 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA A1687 " --> pdb=" O THR A1733 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A1733 " --> pdb=" O ALA A1687 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN A1689 " --> pdb=" O PHE A1731 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE A1731 " --> pdb=" O ASN A1689 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA A1691 " --> pdb=" O ILE A1729 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE A1729 " --> pdb=" O ALA A1691 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N THR A1693 " --> pdb=" O SER A1727 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER A1727 " --> pdb=" O THR A1693 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY A1771 " --> pdb=" O SER A1727 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE A1729 " --> pdb=" O GLY A1769 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLY A1769 " --> pdb=" O ILE A1729 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A1731 " --> pdb=" O GLN A1767 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN A1767 " --> pdb=" O PHE A1731 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR A1733 " --> pdb=" O ASN A1765 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ASN A1765 " --> pdb=" O THR A1733 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE A1735 " --> pdb=" O ALA A1763 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA A1763 " --> pdb=" O ILE A1735 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE A1876 " --> pdb=" O PRO A1961 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASN A1878 " --> pdb=" O VAL A1959 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL A1959 " --> pdb=" O ASN A1878 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASN A1880 " --> pdb=" O GLY A1957 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLY A1957 " --> pdb=" O ASN A1880 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN A1882 " --> pdb=" O ASN A1955 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASN A1955 " --> pdb=" O ASN A1882 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU A1884 " --> pdb=" O THR A1953 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N THR A1953 " --> pdb=" O LEU A1884 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR A1886 " --> pdb=" O ASN A1951 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASN A1951 " --> pdb=" O THR A1886 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A1951 " --> pdb=" O LYS A2016 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP A2034 " --> pdb=" O SER A2068 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A2208 " --> pdb=" O THR A2069 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A2336 " --> pdb=" O LEU A2346 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU A2346 " --> pdb=" O VAL A2336 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN A 246 " --> pdb=" O GLN A 218 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL A 220 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS A 244 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 222 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLY A 242 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 754 " --> pdb=" O ARG A 782 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 145 through 152 Processing sheet with id= C, first strand: chain 'A' and resid 264 through 270 Processing sheet with id= D, first strand: chain 'A' and resid 275 through 282 Processing sheet with id= E, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.778A pdb=" N TYR A 447 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 425 through 428 removed outlier: 23.642A pdb=" N SER A 502 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 19.326A pdb=" N TYR A 466 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 11.710A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 465 through 468 Processing sheet with id= H, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= I, first strand: chain 'A' and resid 527 through 529 Processing sheet with id= J, first strand: chain 'A' and resid 717 through 720 Processing sheet with id= K, first strand: chain 'A' and resid 866 through 869 removed outlier: 3.709A pdb=" N ASP A1194 " --> pdb=" O GLN A1215 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS A1217 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE A1192 " --> pdb=" O LYS A1217 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1250 through 1254 Processing sheet with id= M, first strand: chain 'A' and resid 987 through 993 Processing sheet with id= N, first strand: chain 'A' and resid 1283 through 1291 Processing sheet with id= O, first strand: chain 'A' and resid 1313 through 1315 Processing sheet with id= P, first strand: chain 'A' and resid 1342 through 1348 Processing sheet with id= Q, first strand: chain 'A' and resid 1423 through 1426 removed outlier: 6.407A pdb=" N LEU A1510 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TYR A 857 " --> pdb=" O LEU A1510 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 1739 through 1742 Processing sheet with id= S, first strand: chain 'A' and resid 1848 through 1853 Processing sheet with id= T, first strand: chain 'A' and resid 2027 through 2032 Processing sheet with id= U, first strand: chain 'A' and resid 2044 through 2047 Processing sheet with id= V, first strand: chain 'A' and resid 2215 through 2217 Processing sheet with id= W, first strand: chain 'A' and resid 2264 through 2269 Processing sheet with id= X, first strand: chain 'A' and resid 2276 through 2278 Processing sheet with id= Y, first strand: chain 'A' and resid 1945 through 1949 removed outlier: 6.630A pdb=" N ASN A2020 " --> pdb=" O LYS A1946 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL A1948 " --> pdb=" O THR A2018 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N THR A2018 " --> pdb=" O VAL A1948 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 97 through 99 Processing sheet with id= AA, first strand: chain 'B' and resid 55 through 59 removed outlier: 6.486A pdb=" N GLU B 141 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 90 through 98 Processing sheet with id= AC, first strand: chain 'F' and resid 118 through 120 Processing sheet with id= AD, first strand: chain 'D' and resid 514 through 521 808 hydrogen bonds defined for protein. 2175 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.42 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7242 1.34 - 1.46: 4463 1.46 - 1.57: 10573 1.57 - 1.69: 7 1.69 - 1.81: 90 Bond restraints: 22375 Sorted by residual: bond pdb=" C1 LMN F 501 " pdb=" O5 LMN F 501 " ideal model delta sigma weight residual 1.403 1.566 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" C4 LMN F 501 " pdb=" O4 LMN F 501 " ideal model delta sigma weight residual 1.409 1.508 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" CCF LMN F 501 " pdb=" OBX LMN F 501 " ideal model delta sigma weight residual 1.410 1.498 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" CCS LMN F 501 " pdb=" OBZ LMN F 501 " ideal model delta sigma weight residual 1.394 1.482 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" CCR LMN F 501 " pdb=" OBY LMN F 501 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.77e+01 ... (remaining 22370 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.70: 593 106.70 - 113.53: 11844 113.53 - 120.36: 8149 120.36 - 127.19: 9625 127.19 - 134.01: 168 Bond angle restraints: 30379 Sorted by residual: angle pdb=" N SER D 487 " pdb=" CA SER D 487 " pdb=" C SER D 487 " ideal model delta sigma weight residual 110.80 121.97 -11.17 2.13e+00 2.20e-01 2.75e+01 angle pdb=" CA TYR D 486 " pdb=" C TYR D 486 " pdb=" N SER D 487 " ideal model delta sigma weight residual 118.22 114.54 3.68 1.03e+00 9.43e-01 1.28e+01 angle pdb=" CCQ LMN F 501 " pdb=" OCB LMN F 501 " pdb=" CCS LMN F 501 " ideal model delta sigma weight residual 119.65 109.60 10.05 3.00e+00 1.11e-01 1.12e+01 angle pdb=" C TYR D 486 " pdb=" N SER D 487 " pdb=" CA SER D 487 " ideal model delta sigma weight residual 121.54 127.86 -6.32 1.91e+00 2.74e-01 1.09e+01 angle pdb=" C4 LMN F 501 " pdb=" O4 LMN F 501 " pdb=" CCR LMN F 501 " ideal model delta sigma weight residual 120.22 110.36 9.86 3.00e+00 1.11e-01 1.08e+01 ... (remaining 30374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 12901 23.98 - 47.97: 391 47.97 - 71.95: 71 71.95 - 95.93: 16 95.93 - 119.91: 20 Dihedral angle restraints: 13399 sinusoidal: 5379 harmonic: 8020 Sorted by residual: dihedral pdb=" CA VAL D 463 " pdb=" C VAL D 463 " pdb=" N TYR D 464 " pdb=" CA TYR D 464 " ideal model delta harmonic sigma weight residual 180.00 -142.89 -37.11 0 5.00e+00 4.00e-02 5.51e+01 dihedral pdb=" CA TYR D 486 " pdb=" C TYR D 486 " pdb=" N SER D 487 " pdb=" CA SER D 487 " ideal model delta harmonic sigma weight residual 180.00 148.55 31.45 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA SER D 487 " pdb=" C SER D 487 " pdb=" N LEU D 488 " pdb=" CA LEU D 488 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 13396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2125 0.037 - 0.073: 793 0.073 - 0.110: 273 0.110 - 0.147: 106 0.147 - 0.183: 6 Chirality restraints: 3303 Sorted by residual: chirality pdb=" CA SER D 487 " pdb=" N SER D 487 " pdb=" C SER D 487 " pdb=" CB SER D 487 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CCV LMN F 501 " pdb=" CCR LMN F 501 " pdb=" CCT LMN F 501 " pdb=" OAU LMN F 501 " both_signs ideal model delta sigma weight residual False 2.28 2.45 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA ILE A1007 " pdb=" N ILE A1007 " pdb=" C ILE A1007 " pdb=" CB ILE A1007 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 3300 not shown) Planarity restraints: 4022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1639 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C PHE A1639 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE A1639 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE A1640 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 176 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C SER A 176 " -0.042 2.00e-02 2.50e+03 pdb=" O SER A 176 " 0.016 2.00e-02 2.50e+03 pdb=" N MET A 177 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 605 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 606 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " 0.022 5.00e-02 4.00e+02 ... (remaining 4019 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 395 2.66 - 3.22: 19599 3.22 - 3.78: 33189 3.78 - 4.34: 49517 4.34 - 4.90: 82375 Nonbonded interactions: 185075 Sorted by model distance: nonbonded pdb=" O LYS F 320 " pdb=" OG SER F 346 " model vdw 2.097 2.440 nonbonded pdb=" OH TYR A1015 " pdb=" O ASN A1025 " model vdw 2.205 2.440 nonbonded pdb=" OD1 ASN A 982 " pdb=" OG SER A 984 " model vdw 2.211 2.440 nonbonded pdb=" OD2 ASP A2163 " pdb=" OG SER A2165 " model vdw 2.220 2.440 nonbonded pdb=" O PRO D 465 " pdb=" OG1 THR D 468 " model vdw 2.224 2.440 ... (remaining 185070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.050 Check model and map are aligned: 0.330 Set scattering table: 0.220 Process input model: 61.630 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 22375 Z= 0.309 Angle : 0.583 11.172 30379 Z= 0.309 Chirality : 0.046 0.183 3303 Planarity : 0.004 0.039 4022 Dihedral : 13.071 119.915 8283 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.63 % Allowed : 6.59 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.16), residues: 2743 helix: -1.22 (0.29), residues: 284 sheet: -0.47 (0.16), residues: 1061 loop : -1.06 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.021 0.001 PHE A1009 TYR 0.019 0.001 TYR A1394 ARG 0.002 0.000 ARG A1556 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 346 time to evaluate : 2.535 Fit side-chains REVERT: A 539 ASP cc_start: 0.6512 (t0) cc_final: 0.6173 (t0) REVERT: A 683 LYS cc_start: 0.7873 (mttt) cc_final: 0.7376 (mttp) REVERT: A 745 GLU cc_start: 0.6693 (mm-30) cc_final: 0.6426 (mt-10) REVERT: A 862 GLU cc_start: 0.5995 (OUTLIER) cc_final: 0.5090 (mt-10) REVERT: A 2185 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7796 (m-40) REVERT: A 2343 ASN cc_start: 0.7545 (OUTLIER) cc_final: 0.7339 (t0) REVERT: B 30 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7600 (mt-10) REVERT: B 38 TYR cc_start: 0.8732 (t80) cc_final: 0.8373 (t80) REVERT: B 42 ASN cc_start: 0.8615 (m110) cc_final: 0.8292 (m110) REVERT: B 96 ASN cc_start: 0.7250 (t0) cc_final: 0.6986 (t0) REVERT: B 142 ILE cc_start: 0.9289 (tt) cc_final: 0.9079 (tt) REVERT: F 123 THR cc_start: 0.6650 (OUTLIER) cc_final: 0.5670 (p) REVERT: F 128 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7175 (pt0) REVERT: D 474 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7481 (m-80) REVERT: D 505 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7928 (mm) outliers start: 87 outliers final: 35 residues processed: 411 average time/residue: 0.3562 time to fit residues: 225.5100 Evaluate side-chains 280 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 238 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 862 GLU Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2220 ASP Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2343 ASN Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 514 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 20.0000 chunk 207 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 130 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 437 ASN A 491 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 GLN A1787 ASN A1826 ASN A1874 ASN B 143 GLN ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 22375 Z= 0.513 Angle : 0.669 10.857 30379 Z= 0.345 Chirality : 0.049 0.352 3303 Planarity : 0.004 0.042 4022 Dihedral : 9.730 95.130 3218 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.21 % Allowed : 10.00 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.16), residues: 2743 helix: -1.13 (0.30), residues: 277 sheet: -0.45 (0.16), residues: 1050 loop : -1.14 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1580 HIS 0.009 0.001 HIS D 525 PHE 0.024 0.002 PHE A1480 TYR 0.019 0.002 TYR A1394 ARG 0.005 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 230 time to evaluate : 3.321 Fit side-chains REVERT: A 180 MET cc_start: 0.6759 (mmt) cc_final: 0.6549 (mmt) REVERT: A 2185 ASN cc_start: 0.8117 (OUTLIER) cc_final: 0.7646 (m-40) REVERT: B 25 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8108 (mtmm) REVERT: B 33 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8263 (tppt) REVERT: B 38 TYR cc_start: 0.8776 (t80) cc_final: 0.8424 (t80) REVERT: B 42 ASN cc_start: 0.8616 (m110) cc_final: 0.8400 (m110) REVERT: B 55 TYR cc_start: 0.8881 (p90) cc_final: 0.8589 (p90) REVERT: B 96 ASN cc_start: 0.7334 (t0) cc_final: 0.6960 (t0) REVERT: B 102 LYS cc_start: 0.8534 (tttt) cc_final: 0.8303 (tttt) REVERT: B 113 GLU cc_start: 0.6550 (tp30) cc_final: 0.6114 (tp30) REVERT: F 123 THR cc_start: 0.6615 (OUTLIER) cc_final: 0.5899 (p) REVERT: F 128 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: D 474 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7715 (m-80) outliers start: 101 outliers final: 64 residues processed: 309 average time/residue: 0.3083 time to fit residues: 155.7511 Evaluate side-chains 281 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 213 time to evaluate : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1644 LYS Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1787 ASN Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1874 ASN Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain F residue 385 ASN Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 199 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 437 ASN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1787 ASN A2343 ASN B 96 ASN B 176 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22375 Z= 0.292 Angle : 0.578 10.564 30379 Z= 0.300 Chirality : 0.046 0.333 3303 Planarity : 0.004 0.039 4022 Dihedral : 8.324 73.584 3201 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.71 % Allowed : 11.09 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2743 helix: -0.95 (0.31), residues: 279 sheet: -0.40 (0.16), residues: 1047 loop : -1.04 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1580 HIS 0.006 0.001 HIS D 525 PHE 0.021 0.001 PHE A1009 TYR 0.019 0.001 TYR A 806 ARG 0.005 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 227 time to evaluate : 3.497 Fit side-chains REVERT: A 180 MET cc_start: 0.6774 (mmt) cc_final: 0.6545 (mmt) REVERT: A 1580 TRP cc_start: 0.7595 (OUTLIER) cc_final: 0.6654 (p-90) REVERT: A 2185 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7546 (m-40) REVERT: B 38 TYR cc_start: 0.8730 (t80) cc_final: 0.8454 (t80) REVERT: B 96 ASN cc_start: 0.7421 (t0) cc_final: 0.7159 (t0) REVERT: B 101 TYR cc_start: 0.8509 (p90) cc_final: 0.8240 (p90) REVERT: F 123 THR cc_start: 0.6574 (OUTLIER) cc_final: 0.5677 (p) REVERT: F 128 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7261 (pt0) REVERT: D 474 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: D 532 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7611 (tptm) outliers start: 89 outliers final: 66 residues processed: 297 average time/residue: 0.3188 time to fit residues: 152.9383 Evaluate side-chains 289 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 217 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 995 ASN Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1733 THR Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1787 ASN Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1874 ASN Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain F residue 385 ASN Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 532 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 9.9990 chunk 187 optimal weight: 0.1980 chunk 129 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 chunk 250 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A 752 GLN A1224 GLN A1787 ASN A2248 GLN F 72 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22375 Z= 0.262 Angle : 0.560 10.720 30379 Z= 0.289 Chirality : 0.046 0.338 3303 Planarity : 0.003 0.036 4022 Dihedral : 7.533 73.131 3201 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.83 % Allowed : 11.88 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.16), residues: 2743 helix: -0.88 (0.31), residues: 278 sheet: -0.32 (0.16), residues: 1041 loop : -0.98 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1580 HIS 0.007 0.001 HIS D 525 PHE 0.020 0.001 PHE A1009 TYR 0.023 0.001 TYR A2221 ARG 0.006 0.000 ARG A2207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 225 time to evaluate : 2.597 Fit side-chains REVERT: A 180 MET cc_start: 0.6710 (mmt) cc_final: 0.6485 (mmt) REVERT: A 1580 TRP cc_start: 0.7604 (OUTLIER) cc_final: 0.6667 (p-90) REVERT: A 1765 ASN cc_start: 0.8308 (OUTLIER) cc_final: 0.8096 (m-40) REVERT: A 2185 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7570 (m-40) REVERT: B 38 TYR cc_start: 0.8732 (t80) cc_final: 0.8428 (t80) REVERT: B 96 ASN cc_start: 0.7412 (t0) cc_final: 0.7148 (t0) REVERT: F 123 THR cc_start: 0.6555 (OUTLIER) cc_final: 0.5674 (p) REVERT: F 128 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7234 (pt0) REVERT: D 474 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7569 (m-80) outliers start: 92 outliers final: 66 residues processed: 297 average time/residue: 0.3156 time to fit residues: 152.4310 Evaluate side-chains 289 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 217 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1370 ASN Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1733 THR Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1787 ASN Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 72 GLN Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 385 ASN Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 20.0000 chunk 150 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 109 optimal weight: 0.0770 chunk 226 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 overall best weight: 3.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A1787 ASN A1874 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22375 Z= 0.339 Angle : 0.574 9.885 30379 Z= 0.299 Chirality : 0.046 0.336 3303 Planarity : 0.004 0.036 4022 Dihedral : 7.259 72.464 3198 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.13 % Allowed : 12.34 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2743 helix: -0.90 (0.31), residues: 278 sheet: -0.33 (0.16), residues: 1044 loop : -1.02 (0.16), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1580 HIS 0.006 0.001 HIS D 525 PHE 0.020 0.001 PHE A1009 TYR 0.018 0.001 TYR A2221 ARG 0.006 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 220 time to evaluate : 2.481 Fit side-chains REVERT: A 180 MET cc_start: 0.6663 (mmt) cc_final: 0.6416 (mmt) REVERT: A 752 GLN cc_start: 0.7407 (mt0) cc_final: 0.6810 (mt0) REVERT: A 1580 TRP cc_start: 0.7656 (OUTLIER) cc_final: 0.6732 (p-90) REVERT: A 1765 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8127 (m-40) REVERT: A 2185 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7512 (m-40) REVERT: B 38 TYR cc_start: 0.8735 (t80) cc_final: 0.8413 (t80) REVERT: B 96 ASN cc_start: 0.7422 (t0) cc_final: 0.7155 (t0) REVERT: F 123 THR cc_start: 0.6611 (OUTLIER) cc_final: 0.5669 (p) REVERT: F 128 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7278 (pt0) REVERT: F 242 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6842 (t0) REVERT: D 474 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7651 (m-80) REVERT: D 506 SER cc_start: 0.8380 (m) cc_final: 0.8138 (p) outliers start: 99 outliers final: 76 residues processed: 298 average time/residue: 0.3156 time to fit residues: 152.8226 Evaluate side-chains 291 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 208 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 995 ASN Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1370 ASN Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1787 ASN Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 385 ASN Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 220 optimal weight: 20.0000 chunk 122 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A1387 ASN A1787 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22375 Z= 0.390 Angle : 0.599 9.548 30379 Z= 0.310 Chirality : 0.047 0.335 3303 Planarity : 0.004 0.036 4022 Dihedral : 7.165 71.501 3196 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.88 % Allowed : 13.21 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.16), residues: 2743 helix: -0.92 (0.31), residues: 274 sheet: -0.31 (0.16), residues: 1035 loop : -1.04 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1580 HIS 0.006 0.001 HIS D 525 PHE 0.021 0.002 PHE A1009 TYR 0.016 0.002 TYR A1655 ARG 0.006 0.000 ARG F 388 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 210 time to evaluate : 2.583 Fit side-chains revert: symmetry clash REVERT: A 1580 TRP cc_start: 0.7721 (OUTLIER) cc_final: 0.6902 (p-90) REVERT: A 1765 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8138 (m-40) REVERT: A 2185 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7592 (m-40) REVERT: B 38 TYR cc_start: 0.8742 (t80) cc_final: 0.8411 (t80) REVERT: B 96 ASN cc_start: 0.7403 (t0) cc_final: 0.7139 (t0) REVERT: F 123 THR cc_start: 0.6674 (OUTLIER) cc_final: 0.5771 (p) REVERT: F 128 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7161 (pt0) REVERT: F 242 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6749 (t0) REVERT: D 474 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: D 519 PHE cc_start: 0.8341 (t80) cc_final: 0.8138 (t80) outliers start: 93 outliers final: 77 residues processed: 283 average time/residue: 0.3162 time to fit residues: 146.8827 Evaluate side-chains 288 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 204 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 995 ASN Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1316 ASN Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1370 ASN Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1787 ASN Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 385 ASN Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 193 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 264 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A1787 ASN F 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22375 Z= 0.356 Angle : 0.588 9.460 30379 Z= 0.305 Chirality : 0.047 0.323 3303 Planarity : 0.004 0.037 4022 Dihedral : 7.071 71.125 3195 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.04 % Allowed : 13.30 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.16), residues: 2743 helix: -0.90 (0.31), residues: 274 sheet: -0.32 (0.16), residues: 1030 loop : -1.04 (0.16), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1580 HIS 0.006 0.001 HIS D 525 PHE 0.021 0.002 PHE A1009 TYR 0.020 0.001 TYR A1655 ARG 0.006 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 206 time to evaluate : 2.659 Fit side-chains revert: symmetry clash REVERT: A 1580 TRP cc_start: 0.7740 (OUTLIER) cc_final: 0.6919 (p-90) REVERT: A 1765 ASN cc_start: 0.8381 (OUTLIER) cc_final: 0.8134 (m-40) REVERT: B 38 TYR cc_start: 0.8750 (t80) cc_final: 0.8416 (t80) REVERT: B 96 ASN cc_start: 0.7413 (t0) cc_final: 0.7140 (t0) REVERT: F 123 THR cc_start: 0.6712 (OUTLIER) cc_final: 0.5703 (p) REVERT: F 128 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: F 242 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6748 (t0) REVERT: D 474 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7565 (m-80) outliers start: 97 outliers final: 81 residues processed: 281 average time/residue: 0.3194 time to fit residues: 146.0158 Evaluate side-chains 289 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 202 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 995 ASN Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1129 LEU Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1316 ASN Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1370 ASN Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1787 ASN Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 385 ASN Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 chunk 79 optimal weight: 0.0570 chunk 51 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 240 optimal weight: 10.0000 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A1787 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 22375 Z= 0.407 Angle : 0.611 9.373 30379 Z= 0.317 Chirality : 0.047 0.312 3303 Planarity : 0.004 0.037 4022 Dihedral : 7.098 70.947 3195 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.79 % Allowed : 13.59 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.16), residues: 2743 helix: -0.91 (0.31), residues: 273 sheet: -0.33 (0.16), residues: 1028 loop : -1.07 (0.16), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1580 HIS 0.006 0.001 HIS D 525 PHE 0.022 0.002 PHE A1242 TYR 0.014 0.002 TYR A 604 ARG 0.007 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 206 time to evaluate : 2.958 Fit side-chains revert: symmetry clash REVERT: A 180 MET cc_start: 0.6525 (mmt) cc_final: 0.6229 (mmt) REVERT: A 1580 TRP cc_start: 0.7810 (OUTLIER) cc_final: 0.6996 (p-90) REVERT: A 1765 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8194 (m-40) REVERT: B 38 TYR cc_start: 0.8764 (t80) cc_final: 0.8431 (t80) REVERT: B 96 ASN cc_start: 0.7386 (t0) cc_final: 0.7124 (t0) REVERT: F 123 THR cc_start: 0.6778 (OUTLIER) cc_final: 0.5887 (p) REVERT: F 128 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7209 (pt0) REVERT: F 242 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6792 (t0) REVERT: D 474 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7637 (m-80) outliers start: 91 outliers final: 79 residues processed: 278 average time/residue: 0.3237 time to fit residues: 147.5199 Evaluate side-chains 284 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 199 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 995 ASN Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1316 ASN Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1370 ASN Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1943 THR Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 385 ASN Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 148 optimal weight: 0.1980 chunk 107 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN ** A1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22375 Z= 0.234 Angle : 0.557 9.219 30379 Z= 0.289 Chirality : 0.045 0.293 3303 Planarity : 0.003 0.038 4022 Dihedral : 6.818 70.933 3195 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.25 % Allowed : 14.30 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.16), residues: 2743 helix: -0.79 (0.31), residues: 274 sheet: -0.24 (0.16), residues: 1023 loop : -0.98 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1580 HIS 0.006 0.001 HIS D 525 PHE 0.020 0.001 PHE A1242 TYR 0.011 0.001 TYR A1118 ARG 0.007 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 210 time to evaluate : 2.699 Fit side-chains revert: symmetry clash REVERT: A 1580 TRP cc_start: 0.7702 (OUTLIER) cc_final: 0.6879 (p-90) REVERT: B 38 TYR cc_start: 0.8752 (t80) cc_final: 0.8397 (t80) REVERT: B 96 ASN cc_start: 0.7395 (t0) cc_final: 0.7153 (t0) REVERT: F 123 THR cc_start: 0.6668 (OUTLIER) cc_final: 0.5768 (p) REVERT: F 128 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: F 242 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6660 (t0) REVERT: D 474 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7631 (m-80) outliers start: 78 outliers final: 67 residues processed: 269 average time/residue: 0.3200 time to fit residues: 138.9359 Evaluate side-chains 277 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 205 time to evaluate : 2.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 880 SER Chi-restraints excluded: chain A residue 928 ASP Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1316 ASN Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 385 ASN Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 8.9990 chunk 260 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 251 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN A2248 GLN ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 471 ASN ** D 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 22375 Z= 0.570 Angle : 0.684 11.274 30379 Z= 0.354 Chirality : 0.049 0.302 3303 Planarity : 0.004 0.050 4022 Dihedral : 7.219 71.032 3194 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.38 % Allowed : 14.34 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.16), residues: 2743 helix: -1.00 (0.30), residues: 274 sheet: -0.44 (0.16), residues: 1034 loop : -1.14 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1580 HIS 0.006 0.001 HIS D 525 PHE 0.026 0.002 PHE D 519 TYR 0.020 0.002 TYR A 604 ARG 0.008 0.001 ARG A 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 205 time to evaluate : 2.927 Fit side-chains revert: symmetry clash REVERT: A 1580 TRP cc_start: 0.7924 (OUTLIER) cc_final: 0.7174 (p-90) REVERT: A 1890 MET cc_start: 0.7720 (mmm) cc_final: 0.7512 (mmm) REVERT: B 38 TYR cc_start: 0.8781 (t80) cc_final: 0.8427 (t80) REVERT: B 96 ASN cc_start: 0.7481 (t0) cc_final: 0.7242 (t0) REVERT: F 123 THR cc_start: 0.6900 (OUTLIER) cc_final: 0.6209 (p) REVERT: F 128 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7574 (pt0) REVERT: F 242 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6776 (t70) REVERT: D 474 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7610 (m-80) outliers start: 81 outliers final: 69 residues processed: 268 average time/residue: 0.3488 time to fit residues: 155.9304 Evaluate side-chains 275 residues out of total 2399 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 201 time to evaluate : 2.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 747 ASN Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1258 ASP Chi-restraints excluded: chain A residue 1279 ASP Chi-restraints excluded: chain A residue 1281 ASP Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1291 ASN Chi-restraints excluded: chain A residue 1316 ASN Chi-restraints excluded: chain A residue 1350 SER Chi-restraints excluded: chain A residue 1353 MET Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1370 ASN Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1527 THR Chi-restraints excluded: chain A residue 1542 SER Chi-restraints excluded: chain A residue 1565 ASN Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1999 THR Chi-restraints excluded: chain A residue 2066 SER Chi-restraints excluded: chain A residue 2071 MET Chi-restraints excluded: chain A residue 2136 ASN Chi-restraints excluded: chain A residue 2185 ASN Chi-restraints excluded: chain A residue 2219 PHE Chi-restraints excluded: chain A residue 2247 GLU Chi-restraints excluded: chain A residue 2264 ARG Chi-restraints excluded: chain A residue 2335 LEU Chi-restraints excluded: chain A residue 2341 TYR Chi-restraints excluded: chain A residue 2358 THR Chi-restraints excluded: chain A residue 2360 ASP Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 101 ASN Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 ASP Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 199 ASN Chi-restraints excluded: chain F residue 242 ASP Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 385 ASN Chi-restraints excluded: chain F residue 392 THR Chi-restraints excluded: chain D residue 460 ASP Chi-restraints excluded: chain D residue 468 THR Chi-restraints excluded: chain D residue 469 LYS Chi-restraints excluded: chain D residue 474 PHE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 0.9990 chunk 231 optimal weight: 0.0040 chunk 66 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 32 optimal weight: 0.0370 chunk 60 optimal weight: 0.3980 chunk 217 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.4874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 339 ASN ** A1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1205 ASN A1210 ASN A2248 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.073121 restraints weight = 41496.010| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.81 r_work: 0.2823 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22375 Z= 0.142 Angle : 0.560 10.773 30379 Z= 0.290 Chirality : 0.045 0.275 3303 Planarity : 0.003 0.042 4022 Dihedral : 6.686 70.958 3194 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.54 % Allowed : 15.26 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2743 helix: -0.74 (0.32), residues: 274 sheet: -0.21 (0.16), residues: 1023 loop : -0.97 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2353 HIS 0.005 0.001 HIS D 525 PHE 0.022 0.001 PHE D 519 TYR 0.016 0.001 TYR A1655 ARG 0.008 0.000 ARG A 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4503.98 seconds wall clock time: 83 minutes 8.24 seconds (4988.24 seconds total)